## [1] "test_dataset1_2.hicup.bam"
Truncation & Mapping
Truncation Frequency
| Total |
99,742 |
99,742 |
| Not Truncated |
92,512 |
92,628 |
| Truncated |
7,230 |
7,114 |
Truncated Read Length
| Average Length Truncated |
22.4 |
22.6 |
Mapping Efficiency
| Too Short To Map |
2,658 |
2,476 |
| Unique Alignments |
3,885 |
3,725 |
| Multiple Alignments |
12,437 |
12,679 |
| Failed To Align |
80,762 |
80,862 |
| Paired |
1,143 |
1,143 |
Truncation and Mapping Bar Plot
Filtering
Filtering Breakdown by Category
| Valid Pairs |
401 |
| Invalid Pairs |
742 |
| Same Circularised |
21 |
| Same Dangling Ends |
73 |
| Same Fragment Internal |
466 |
| Re Ligation |
39 |
| Contiguous Sequence |
3 |
| Wrong Size |
140 |
| Total Pairs |
1,143 |
Filtering Breakdown Pie Chart
Ditag Length Distribution
Deduplication
Deduplication Summary Table
| Read Pairs |
401 |
401 |
| Cis-close (<10Kbp) |
36 |
36 |
| Cis-far (>10Kbp) |
346 |
346 |
| Trans |
19 |
19 |
Deduplication Bar Chart
Analysis produced by HiCUP - a tool for mapping and performing
quality control on Hi-C data
